Staff information
James Carson
Systems Toxicology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/371-6894
Send Email
Research Interests
- Spatial organization of biological information
Education and Credentials
- B.S. & M.E.E. from Rice University's Department of Electrical Engineering
- Ph.D. from Baylor College of Medicine's Program in Structural and Computational Biology & Molecular Biophysics
Affiliations and Professional Service
- IEEE
- Society of Neuroscience
PNNL Publications
2013
- Einstein DR, AP Kuprat, X Jiao, JP Carson, DM Einstein, RA Corley, and RE Jacob. 2013. "An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics." International Journal for Numerical Methods in Biomedical Engineering 29(1):1-16. doi:10.1002/cnm.2489
- Kleese van Dam K, JP Carson, AL Corrigan, DR Einstein, ZC Guillen, BS Heath, AP Kuprat, IT Lanekoff, CS Lansing, J Laskin, D Li, Y Liu, MJ Marshall, EA Miller, G Orr, P Pinheiro da Silva, S Ryu, CJ Szymanski, and M Thomas. 2013. "Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities." In Proceedings of the IEEE 8th International Conference on EScience, October 8-12, 2012, Chicago, Illinois. IEEE Press, Los Alamitos, CA. doi: 10.1109/eScience.2012.6404463
- Lanekoff IT, M Thomas, JP Carson, JN Smith, C Timchalk, and J Laskin. 2013. "Imaging Nicotine in Rat Brain Tissue by Use of Nanospray Desorption Electrospray Ionization Mass Spectrometry." Analytical Chemistry 85(2):882-889. doi:10.1021/ac302308p
2012
- Corley RA, S Kabilan, AP Kuprat, JP Carson, KR Minard, RE Jacob, C Timchalk, RW Glenny, S Pipavath, TC Cox, C Wallis, R Larson, M Fanucchi, E Postlewait, and DR Einstein. 2012. "COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN." Toxicological Sciences 128(2):500-516. doi:10.1093/toxsci/kfs168
- Freed AD, DR Einstein, JP Carson, and RE Jacob. 2012. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System, Phase II: Dodecahedral Micro-Model. PNNL-21287, Pacific Northwest National Laboratory, Richland, WA.
- Lanekoff IT, BS Heath, AV Liyu, M Thomas, JP Carson, and J Laskin. 2012. "An Automated Platform for High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry." Analytical Chemistry 84(19):8351-8356.
- Minard KR, AP Kuprat, S Kabilan, RE Jacob, DR Einstein, JP Carson, and RA Corley. 2012. "Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways." Journal of Magnetic Resonance 221:129-138. doi:10.1016/j.jmr.2012.05.007
- Neradilek MB, N Polissar, DR Einstein, RW Glenny, KR Minard, JP Carson, X Jiao, RE Jacob, TC Cox, E Postlewait, and RA Corley. 2012. "BRANCH-BASED MODEL FOR THE DIAMETERS OF THE PULMONARY AIRWAYS: ACCOUNTING FOR DEPARTURES FROM SELF-CONSISTENCY AND REGISTRATION ERRORS." The Anatomical Record 295(6):1027-1044. doi:10.1002/ar.22476
2011
- Kindle LM, I Kakadiaris, T Ju, and JP Carson. 2011. "A semiautomated approach for artefact removal in serial tissue cryosections." Journal of Microscopy 241(2):200-206. doi:10.1111/j.1365-2818.2010.03424.x
- Enlow MA, T Ju, I Kakadiaris, and JP Carson. 2011. "Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain." In Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2011), August 30-September 3, 2011, Boston, Massachusetts, pp. 8086-8089. IEEE, Piscataway, NJ.
- Kurkure U, YH Le, N Paragios, JP Carson, T Ju, and I Kakadiaris. 2011. "Landmark/Image-based Deformable Registration of Gene Expression Data." In IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011), June 20-25, 2011, Colorado Springs, Colorado, pp. 1089-1096. IEEE Computer Society, Los Alamitos, CA. doi:10.1109/CVPR.2011.5995708
- Kurkure U, YH Le, N Paragios, T Ju, JP Carson, and I Kakadiaris. 2011. "Markov Random Field-Based Fitting of a Subdivision-Based Geometric Atlas." In IEEE International Conference on Computer Vision (ICCV), November 6-13, 2011, Barcelona, Spain, pp. 2540-2547. IEEE, Piscataway, NJ. doi:10.1109/ICCV.2011.6126541
2010
- Carson JP, T Ju, M Bello, C Thaller, J Warren, I Kakadiaris, W Chiu, and G Eichele. 2010. "Automated pipeline for atlas-based annotation of gene expresssion patterns: application to postnatal day 7 mouse brain." Methods, A Companion to Methods in Enzymology 50(2):85-95.
- Carson JP, DR Einstein, KR Minard, M Fanucchi, C Wallis, and RA Corley. 2010. "High resolution lung airway cast segmentation with proper topology suitable for computational fluid dynamic simulations." Computerized Medical Imaging and Graphics 34(7):572-857. doi:10.1016/j.compmedimag.2010.03.001
- Carson JP, AP Kuprat, X Jiao, F del Pin, and DR Einstein. 2010. "An Anisotropic Fluid-Solid Model of the Mouse Heart." In Computers in Cardiology 2009, Park City, Utah September 13-16, 2009, vol. 36, pp. 377-380. Computers in Cardiology and IEEE, Piscataway, NJ.
- Carson JP, AP Kuprat, X Jiao, V Dyedov, F del Pin, JM Guccione, MB Ratcliffe, and DR Einstein. 2010. "Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations." Biomechanics and Modeling in Mechanobiology 9(2):187-201. doi:10.1007/S10237-009-0170-5
- Ju T, JP Carson, L Liu, J Warren, M Bello, and I Kakadiaris. 2010. "Subdivision meshes for organizing spatial biomedical data. ." Methods 50(2):70-76. doi:10.1016/J.YMETH.2009.07.012
2009
- Einstein DR, F del Pin, X Jiao, AP Kuprat, JP Carson, K Kunzelman, RP Cochran, JM Guccione, and MB Ratcliffe. 2009. "Fluid-Structure Interactions of the Mitral Valve and Left Heart: Comprehensive Strategies, Past, Present and Future." International Journal for Numerical Methods in Biomedical Engineering 26(3-4):348-380. doi:10.1002/cnm.1280
- Jacob RE, JP Carson, KM Gideon, BG Amidan, CL Smith, and KM Lee. 2009. "Comparison of Two Quantitative Methods of Discerning Airspace Enlargement in Smoke-Exposed Mice." PLoS One 4(8):E6670. doi:10.1371/journal.pone.0006670
- Dyedov V, DR Einstein, X Jiao, AP Kuprat, JP Carson, and F del Pin. 2009. "Variational Generation of Prismatic Boundary-Layer Meshes for Biomedical Computing." International Journal for Numerical Methods in Engineering 79(8):907-945. doi:10.1002/nme.2583
- Jiao X, DR Einstein, V Dyedov, and JP Carson. 2009. "Automatic Identification and Truncation of Boundary Outlets in Complex Imaging-Derived Biomedical Geometries." Medical & Biological Engineering & Computing 47(9):989-999. doi:10.1007/s11517-009-0501-9
2008
- Einstein DR, B Neradilak, N Pollisar, KR Minard, C Wallis, M Fanucchi, JP Carson, AP Kuprat, S Kabilan, R Jacob, and R Corley. 2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291(12):1628-1648. doi:10.1002/ar.20771
- Gatchel JR, K Watase, C Thaller, JP Carson, P Jafar-Nejad, CA Shaw, T Zu, HT Orr, and HY Zoghbi. 2008. "The insulin-like growth factor pathway is altered in Spinocerebellar ataxia type 1 and type 7." Proceedings of the National Academy of Sciences of the United States of America 105(4):1291-1296. doi:10.1073/pnas.0711257105
2007
- Bello M, T Ju, JP Carson, J Warren, W Chiu, and I Kakadiaris. 2007. "Learning-based Segmentation Framework for Tissue Images Containing Gene Expression Data." IEEE Transactions on Medical Imaging 26(5):728-744. doi:10.1109/TMI.2007.895462
- Visel A, JP Carson, J Oldekamp, M Warnecke, V Jakubcakova, X Zhou, C Shaw, G Alvarez-Bolado, and G Eichele. 2007. "Regulatory pathway analysis by high-throughput in situ hybridization." PLoS Genetics 3(10):paper no. e178. doi:10.1371/journal.pgen.0030178
2006
- Ju T, J Warren, JP Carson, M Bello, I Kakadiaris, W Chiu, C Thaller, and G Eichele. 2006. "3D volume reconstruction of a mouse brain histological sections using warp filtering." Journal of Neuroscience Methods 156(1-2):84-100. doi:10.1016/j.jneumeth.2006.02.020